It's important to keep your dog's whelping area -- the place where the mother dog (dam) gives birth to her puppies, and later nurses them -- clean and sanitary. While you should have diluted betadine solution on hand to disinfect the newborn's umbilical cord stump, that's not recommended for cleaning the surfaces of the whelping area. An over-the-counter product, chlorhexidine solution, should suffice to disinfect most whelping places.
Chlorhexidine solution, available at pet stores or online veterinary supply companies, safely disinfects the whelping area but won't harm newborn puppies. While it effectively eliminates most fungus and bacteria and some viruses, it won't kill the potentially deadly parvovirus. If your vet thinks parvovirus is a threat to your puppies prior to their initial shots at the age of six weeks, a bleach dilution of 1 ounce bleach to one gallon of water can be used. A dilution of 4 ounces bleach to a gallon of water for tougher jobs can result in puppy skin irritation, so use it only following veterinary advice.